1urx
From Proteopedia
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| - | [[Image:1urx.gif|left|200px]]<br /><applet load="1urx" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1urx, resolution 1.7Å" /> | ||
| - | '''CRYSTALLOGRAPHIC STRUCTURE OF BETA-AGARASE A IN COMPLEX WITH OLIGOAGAROSE'''<br /> | ||
| - | == | + | ==Crystallographic structure of beta-agarase A in complex with oligoagarose== |
| + | <StructureSection load='1urx' size='340' side='right'caption='[[1urx]], [[Resolution|resolution]] 1.70Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1urx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zobellia_galactanivorans Zobellia galactanivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1URX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1URX FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAL:3,6-ANHYDRO-L-GALACTOSE'>AAL</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1urx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1urx OCA], [https://pdbe.org/1urx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1urx RCSB], [https://www.ebi.ac.uk/pdbsum/1urx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1urx ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/AGAA_ZOBGA AGAA_ZOBGA] Cleaves the beta-1,4-linkages between beta-D-galactose and alpha-L-3,6-anhydro-galactose residues in agarose. Cleaves agarose in a random manner with retention of the anomeric-bond configuration, producing beta-anomers that give rise progressively to alpha-anomers when mutarotation takes place.<ref>PMID:15456406</ref> | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ur/1urx_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1urx ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
Agarose is a gel-forming polysaccharide with an alpha-L(1,4)-3,6-anhydro-galactose, beta-D(1,3)-galactose repeat unit, from the cell walls of marine red algae. beta-agarase A, from the Gram-negative bacterium Zobellia galactanivorans, is secreted to the external medium and degrades agarose with an endo-mechanism. The structure of the inactive mutant beta-agarase A-E147S in complex with agaro-octaose has been solved at 1.7 A resolution. Two oligosaccharide chains are bound to the protein. The first one resides in the active site channel, spanning subsites -4 to -1. A second oligosaccharide binding site, on the opposite side of the protein, was filled with eight sugar units, parallel to the active site. The crystal structure of the beta-agarase A with agaro-octaose provides detailed information on agarose recognition in the catalytic site. The presence of the second, parallel, binding site suggests that the enzyme might be able to unwind the double-helical structure of agarose prior to the catalytic cleavage. | Agarose is a gel-forming polysaccharide with an alpha-L(1,4)-3,6-anhydro-galactose, beta-D(1,3)-galactose repeat unit, from the cell walls of marine red algae. beta-agarase A, from the Gram-negative bacterium Zobellia galactanivorans, is secreted to the external medium and degrades agarose with an endo-mechanism. The structure of the inactive mutant beta-agarase A-E147S in complex with agaro-octaose has been solved at 1.7 A resolution. Two oligosaccharide chains are bound to the protein. The first one resides in the active site channel, spanning subsites -4 to -1. A second oligosaccharide binding site, on the opposite side of the protein, was filled with eight sugar units, parallel to the active site. The crystal structure of the beta-agarase A with agaro-octaose provides detailed information on agarose recognition in the catalytic site. The presence of the second, parallel, binding site suggests that the enzyme might be able to unwind the double-helical structure of agarose prior to the catalytic cleavage. | ||
| - | + | Parallel substrate binding sites in a beta-agarase suggest a novel mode of action on double-helical agarose.,Allouch J, Helbert W, Henrissat B, Czjzek M Structure. 2004 Apr;12(4):623-32. PMID:15062085<ref>PMID:15062085</ref> | |
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| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 1urx" style="background-color:#fffaf0;"></div> | |
| - | [[Category: | + | == References == |
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Zobellia galactanivorans]] | [[Category: Zobellia galactanivorans]] | ||
| - | [[Category: Allouch | + | [[Category: Allouch J]] |
| - | [[Category: Czjzek | + | [[Category: Czjzek M]] |
| - | [[Category: Helbert | + | [[Category: Helbert W]] |
| - | [[Category: Henrissat | + | [[Category: Henrissat B]] |
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Current revision
Crystallographic structure of beta-agarase A in complex with oligoagarose
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